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Update terra-jupyter-aou to Hail 0.2.128 #476

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merged 6 commits into from
Mar 20, 2024
Merged

Update terra-jupyter-aou to Hail 0.2.128 #476

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7c7f539
Update terra-jupyter-aou to Hail version 0.2.127
hail-tester1 Jan 12, 2024
7aea1c9
Update Dockerfile
Feb 20, 2024
0b9da48
Update CHANGELOG.md
Feb 20, 2024
e35206d
Update CHANGELOG.md
Feb 20, 2024
edaca9b
update plink2 path
LizBaldo Mar 20, 2024
9f2bf51
Merge branch 'master' into update-terra-jupyter-aou-to-hail-0.2.127
LizBaldo Mar 20, 2024
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2 changes: 1 addition & 1 deletion config/conf.json
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Expand Up @@ -135,7 +135,7 @@
"r"
],
"packages" : {},
"version" : "2.2.8",
"version" : "2.2.9",
"automated_flags" : {
"include_in_ui" : false,
"generate_docs" : false,
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6 changes: 6 additions & 0 deletions terra-jupyter-aou/CHANGELOG.md
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@@ -1,3 +1,9 @@
## 2.2.9 - 2024-01-12
- Update `hail` to `0.2.128`
- See https://hail.is/docs/0.2/change_log.html#version-0-2-128) for details

Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-aou:2.2.9`

## 2.2.8 - 2023-11-14T15:56:44.507726350Z

- Update `terra-jupyter-gatk` to `2.3.6`
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4 changes: 2 additions & 2 deletions terra-jupyter-aou/Dockerfile
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Expand Up @@ -47,7 +47,7 @@ ENV PYTHONPATH $PYTHONPATH:/usr/lib/spark/python

ENV PYSPARK_PYTHON=python3

ENV HAIL_VERSION=0.2.126
ENV HAIL_VERSION=0.2.128

RUN find $JUPYTER_HOME/scripts -name '*.sh' -type f | xargs chmod +x \
&& $JUPYTER_HOME/scripts/kernel/kernelspec.sh $JUPYTER_HOME/scripts/kernel /opt/conda/share/jupyter/kernels \
Expand Down Expand Up @@ -95,7 +95,7 @@ RUN mkdir -p /tmp/plink && \

RUN mkdir -p /tmp/plink2 && \
cd /tmp/plink2 && \
curl -fsSL -o plink2.zip "https://s3.amazonaws.com/plink2-assets/alpha2/plink2_linux_x86_64.zip" && \
curl -fsSL -o plink2.zip "https://s3.amazonaws.com/plink2-assets/plink2_linux_x86_64_latest.zip" && \
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@Qi77Qi or @yonghaoy the previous path for plink2 was removed, this is the closest that I could find, but could you double check?

unzip plink2.zip && \
mv plink2 /bin/plink2 && \
cd $HOME && \
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